There is a knock at the door early on in my interview with Nobel prize-winning cell biologist Randy Schekman at his office at the University of California, Berkeley, overlooking San Francisco Bay. The 2014 Nobel prize in physiology or medicine was announced in the early hours, California time, and one of his colleagues is calling by for a gossip. “[This time] I actually slept throughout,” says Schekman.

Schekman shared the 2013 prize with James Rothman of Yale University and Thomas Südhof of Stanford University for his role in working out how cells, the smallest units of life, transport and secrete proteins. Those proteins are much-needed molecules such as hormones, digestive enzymes and neurotransmitters. Schekman’s share of the prize was for discovering a set of genes required for transporting the proteins through and out of the cell in the small packages – called vesicles – in which they hitch a ride.

Schekman didn’t bask in the glory. Instead, he decided to speak out about what he sees as the distorting effect elite journals have on the scientific enterprise. To coincide with the acceptance of his prize in Sweden he used Facebook and Twitter to start discussions about how the traditional publishing process needed to change. He wrote an opinion piece in the Guardian, declaring his lab would no longer send papers to the “luxury” journals Nature, Cell and Science, and urging others to do the same. Pressure to publish in elite journals was encouraging researchers to cut corners and pursue trendy scientific fields over more important work, he said.

Schekman, 65, was born in St Paul, Minnesota, and moved to the greater LA area when he was 10, after his father, an engineer, landed a job in its nascent computer industry. A microscope – which Schekman saved up to buy, to replace a toy one that had first revealed the microbial wonders of pond scum – became his “constant companion” throughout high school.

In 1966 he entered UCLA on a medical school track, but left with a degree in molecular biology. From there he won a place at Stanford, to do a PhD in its biochemistry department, under renowned biochemist Arthur Kornberg.

Obtaining his PhD in 1974, Schekman spent the next two years as a researcher at the University of California, San Diego, studying the structure of cell membranes. It was here that he heard a talk by the pioneering cell biologist George Palade that would shape his career. Palade had won a Nobel prize in 1974 for work on how cells secrete proteins. Schekman was impressed, but also felt there was more to find out. “The process clearly had a lot of underlying molecular mechanisms but there was nothing known about them,” says Schekman.

In 1976, as an assistant professor at Berkeley, he was now in a position to start his own research. He decided to take Palade’s work further by identifying the mechanisms by which cells directed vesicles, which carry proteins from the compartment where they are synthesised to another where they are processed and sorted, and finally to the plasma membrane, where they are released to the outside world. He decided to do so by studying cells of baker’s yeast – the single-celled organism used in baking bread.

He finally secured funding and selected a novel genetic approach: he would chemically induce genetic mutations in yeast cells, then isolate those mutant cells that had malfunctions in the transport and secretory system. They would, for example, be unable to secrete an enzyme such as invertase, which yeast cells produce to help them digest sugar. It would then be possible using standard genetic tests to identify the genes crucial to the transport and secretion process. To have the best chance of success he and his graduate student focused on so-called temperature-sensitive mutants, whose defects only become apparent at high temperatures. They sifted through 100 of them until they found two with the right kind of defects.

The eureka moment came in 1978, when they looked under the electron microscope at one of the secretion-defective mutants. “The images were astonishing,” Schekman recalls. “Nothing like this had ever been seen before.” The cell had an enormous number of protein-laden vesicles that could not be discharged. “It was dying of constipation,” he says. The cell had also stopped growing, confirming Schekman’s prediction that protein secretion and cell growth had the same genetic roots. “It was that crucial prediction that was so novel,” he says. “It isn’t necessarily obvious, because the enzymes whose secretion we are studying are themselves not essential for growth.”

Schekman named the gene Sec1 (short for secretory) and, along with a second gene corresponding to another secretion defective mutant, published the discovery in a 1979 paper later highlighted by the Nobel committee. Schekman and his assistant then developed a more efficient method, and uncovered 21 further genes involved in transport and secretion. “We stopped after the 23rd, because I thought: let’s focus on trying to figure out what they do,” he says, though he ultimately identified nearly 50, along with the specific steps in vesicle transport that they mediate. (At least 100 genes in yeast and many hundreds in mammals are today known to be involved in the process.)

Schekman was confident what he had found would also apply to mammalian cells, but proof did not arrive until 1989, when his fellow Nobel prize-winner James Rothman revealed that protein machinery he had found separately in hamster cells which permitted vesicles’ cargo to be transferred was encoded by genes that were equivalent in yeast. “That was an amazing result at the time,” says Schekman. “Here you have a billion years of evolution separating humans from yeast, and yet secretory genes will look the same and even work the same.” That link paved the way for using yeast as a model for studying various human genetic diseases involving problems with protein transport in cells – for example, forms of diabetes and haemophilia.

Schekman’s findings proved valuable to the biotechnology industry. From 1982, Schekman spent 20 years as a consultant to local company Chiron Corporation, now part of drug maker Novartis, helping them to engineer yeast cells to produce insulin and hepatitis B vaccine. Today, one-third of the insulin used worldwide by diabetics, and the entire world’s supply of the hepatitis B vaccine, is produced from yeast using systems developed by the company, with Schekman’s advice. It never occurred to Schekman to commercialise the discovery himself. “I was interested in understanding how a cell works,” he says.

Today, he mostly studies genetic diseases, such as inherited forms of Alzheimer’s, where problems with cell protein transport are implicated.

He is also busy building up the open-access web journal eLife, of which he has been editor-in-chief since its launch in 2012. It is a “superior platform” for publishing the most important work in the life sciences, he says, though he concedes it is yet to pose much competition to the elite journals. “Many young scholars still believe their future depends on securing precious space in one,” he says.

Yet he is patient – it is still early days, submissions are growing and he doesn’t doubt there is room at the top for a different way.

10 QUESTIONS: RANDY SCHEKMAN

What is the most exciting field of science at the moment?Neuroscience. There is so much that we don’t know about the brain.

Do you believe in God?No, I don’t. But I respect others who do, in particular if they don’t impose their views. I believe strongly in the separation of church and state.

What book about science should everyone read?People who are interested in the life sciences will enjoy The Double Helix by James Watson; The Eighth Day of Creation by Horace Judson (it covers the history of molecular biology), and The Statue Within, the autobiography of Nobel laureate François Jacob (right), which is beautifully written.

Has Cern been worth the money?Yes. Just the idea that you can probe the structure of atoms to that degree… Look at all the money we waste on the military, on the prison system.

What words of advice would you give to a teenager who wants a career in science?I think having a mentor from an early age is very important.

Do you have a fantasy experiment or study that you have been unable to do for logistical/ethical/ cost reasons?No. I like the simple experiments and my ideas tend to be very practical. Our very first experiments involved petri dishes, incubators, toothpicks and simple chemicals.

What scientific advance would make the most difference to your daily life?My wife has dementia, so breakthroughs in understanding Parkinson’s disease would change my daily life measurably. With a disease like Parkinson’s or Alzheimer’s, if you had a way of arresting the process – even if you couldn’t prevent it – it would not be a disease at all.

Are you worried about population increase?Yes. Having effective birth control is crucial. And our agricultural productivity will not keep up unless people lose their irrational fear of GM foods.

Would you like to go on the first one-way journey to Mars?No. I like it here on Earth, and besides, the trip itself would almost inevitably kill you, because of all the exposure to cosmic radiation.

If I called you a geek would you hold it against me?No. When I was in high school I got called a nerd. But after I won the Nobel prize they invited me back. I rode up in a limousine and was greeted by a marching band and pompom girls. Kids wanted to take selfies with me. I had replaced Tiger Woods as their most famous graduate… for a day!